August 16, 2020

Today’s quite diverse digest features: a study on antimicrobial resistance in the drinking water microbiome in disinfected and disinfection-free drinking water systems, how Antarctic soil microorganisms stay energised and hydrated, and several awesome webinars and podcasts. Happy reading/listening!

General microbiome

Development of Microbiome Biobanks – Challenges and Opportunities – M.J. Ryan – Trends in Microbiology

Review: STROBE-metagenomics: a STROBE extension statement to guide the reporting of metagenomics studies – Tehmina Bharucha – The Lancet Infectious Diseases

Theme issue: The role of the microbiome in host evolution – compiled and edited by Oren Kolodny, Benjamin J. Callahan and Angela E. Douglas – Philosophical Transactions of the Royal Society B: Biological Sciences

Selected papers:
Review: Microbiota–host interactions shape ageing dynamics – Miriam Popkes and Dario Riccardo Valenzano – Philosophical Transactions of the Royal Society B: Biological Sciences

Opinion: Pathogen resistance may be the principal evolutionary advantage provided by the microbiome – Michael R. McLaren and Benjamin J. Callahan – Philosophical Transactions of the Royal Society B: Biological Sciences

Gut microbiome

A Randomized Clinical Trial of Fecal Microbiota Transplant for Alcohol Use Disorder – Jasmohan S Bajaj – Hepatology

Urogenital microbiome

Comparative Genomic Study of Lactobacillus jensenii and the Newly Defined Lactobacillus mulieris Species Identifies Species-Specific Functionality – Catherine Putonti – mSphere

Vaginal Estrogen Therapy Is Associated with Increased Lactobacillus in the Urine of Post-Menopausal Women with OAB Symptoms – Dr. Krystal Thomas-White – American Journal of Obstetrics and Gynecology

Vaginal microbiome

Vaginal microbiota, genital inflammation, and neoplasia impact immune checkpoint protein profiles in the cervicovaginal microenvironment – Paweł Łaniewski –npj Precision Oncology

Lateral Gene Transfer Shapes Diversity of Gardnerella spp. – Lindsey L. Bohr – Frontiers in Cellular and Infection Microbiology

Variation of the vaginal microbiome during and after pregnancy in Chinese women – Xiaoai Zhang – medRxiv

Review: Diversity of Vaginal Microbiome in Pregnancy: Deciphering the Obscurity – Parakriti Gupta – Frontiers in Public Health

Pregnancy and early life

Evidence for contamination as the origin for bacteria found in human placenta rather than a microbiota – Rémi Gschwind – PlosOne

Respiratory microbiome

A Novel Description of the Human Sinus Archaeome During Health and Chronic Rhinosinusitis – Brett Wagner Mackenzie – Frontiers in Cellular and Infection Microbiology

Animal microbiome

Temporal changes in the gut microbiota in farmed Atlantic cod (Gadus morhua) outweigh the response to diet supplementation with macroalgae – Ciara Keating – bioRxiv

Broiler Chickens and Early Life Programming: Microbiome transplant-induced cecal bacteriome dynamics and phenotypic effects – Gustavo A. Ramírez – bioRxiv

Rumen metaproteomics: Closer to linking rumen microbial function to animal productivity traits – Thea Os Andersen – Methods

Fast and Slow-Growing Management Systems: Characterisation of Broiler Caecal Microbiota Development throughout the Growing Period – Laura Montoro-Dasi – animals

Animal experiment

Mucosal or systemic microbiota exposures shape the B cell repertoire – Hai Li – Nature

The immune system fails to mount a protective response to Gram-positive or Gram-negative bacterial prostatitis – Federico Lupo – bioRxiv

Oncogenic Gene Fusions in Non-Neoplastic Precursors as Evidence that Bacterial Infection Initiates Prostate Cancer – Eva Shrestha – bioRxiv

Microbiome-derived inosine modulates response to checkpoint inhibitor immunotherapy – Lukas F. Mager – Science

Lung and gut microbiota are altered by hyperoxia and contribute to oxygen-induced lung injury in mice – Shanna L. Ashley – Science Translational Medicine

Plant/root/soil microbiome

*A genome compendium reveals diverse metabolic adaptations of Antarctic soil microorganisms – Maximiliano Ortiz – bioRxiv

Healthy soils for healthy plants for healthy humans – Heribert Hirt – EMBO reports

The Impact of Mercury Selection and Conjugative Genetic Elements on Community Structure and Resistance Gene Transfer – James P. J. Hall – Frontiers in Microbiology

Review: Plant–microbiome interactions: from community assembly to plant health – Pankaj Trivedi – Nature Reviews Microbiology

Water microbiome

*Differential prevalence and host-association of antimicrobial resistance traits in disinfected and non-disinfected drinking water systems – Maria Sevillano – Science of The Total Environment

MiDAS 3: An ecosystem-specific reference database, taxonomy and knowledge platform for activated sludge and anaerobic digesters reveals species-level microbiome composition of activated sludge – Marta Nierychlo – Water Research

Metagenomic profiling of ammonia- and methane-oxidizing microorganisms in two sequential rapid sand filters – Lianna Poghosyan – Water Research

Shotgun metagenomics of indigenous bacteria collected from the banks of the San Jacinto River for biodegradation of aromatic waste – Rupa Iyer and Ashish Damania – FEMS Microbiology Letters

Viruses and phages

Viruses in wastewater: occurrence, abundance and detection methods – Mary Vermi Aizza Corpuz – Science of The Total Environment

Viromes outperform total metagenomes in revealing the spatiotemporal patterns of agricultural soil viral communities – Christian Santos-Medellin – bioRxiv

Techniques

Correlative Light Electron Ion Microscopy reveal in vivo localisation of bedaquiline in Mycobacterium tuberculosis infected lungs – Antony Fearns – bioRxiv

Label-free smartphone quantitation of bacteria by darkfield imaging of light scattering in fluoropolymer micro capillary film allows portable detection of bacteriophage lysis – Sultan İlayda Dönmez – Sensors and Actuators B: Chemical

Bioinformatics

Raven: a de novo genome assembler for long reads – Robert Vaser and Mile Sikic – bioRxiv

SHAMAN: a user-friendly website for metataxonomic analysis from raw reads to statistical analysis – Stevenn Volant – BMC Bioinformatics

Rapid discovery of novel prophages using biological feature engineering and machine learning – Kimmo Sirén – bioRxiv

Critical Relevance of Stochastic Effects on Low-Bacterial Biomass 16S rRNA Gene Analysis – John R. Erb-Downward – mBio

On the complexity of haplotyping a microbial community – Samuel M Nicholls – bioRxiv

Inclusion of Oxford Nanopore long reads improves all microbial and viral metagenome‐assembled genomes from a complex aquifer system – Will A. Overholt – Environmental Microbiology

Webinar

Microbiome, machine learning and network models – Amy Willis and Ben Bloem-Reddy – Northwest Data Science Seminar Series

The Gut Brain Axis across the Life Span – John Cryan – iScience webinar

Pushing the Envelope: Remodeling the Gram-negative Outer Membrane – M. Stephen Trent – SG BUG (Singapore Bacterial Ultra Group) seminar series

Podcast

Getting to Know Your Friendly Neighbourhood Microbiologist – Lucie Semenec and Amy Cain – The Joint Academic Microbiology Seminars podcast

Does not compute – Sanjay Srivastava, Alexa Tullett, and Simine Vazire – The Black Goat podcast

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